Reformat your SD card, then make sure you always use the safely remove hardware option. If you already do that, something else is going on, but not using safely remove would be one way to get corrupted files, so try and see if it helps.

Try these steps:[*]Use the Panasonic formatter to reformat your microSD card: http://panasonic.jp/support/global/cs/sd/d..._formatter.html[*]Grab the official 1.17 menu from here: (but do NOT install TTMENU.DAT from it as it contains the fake-killer code!!!): http://gbatemp.net/index.php?download=4476[*]Copy the TTMENU folder (but not TTMENU.DAT) from the official firmware to your microSD card.[*]Grab this archive: http://gbatemp.net/index.php?download=4086[*]Copy all four files from the archive to your microSD card.[*]Make a folder named "games" on your microSD card. Copy 2 or 3 games (.nds files) to the new "games" folder.[*]Run "safely remove hardware", select your microSD reader in the list, and press STOP before removing your microSD card from your PC.[*]Insert your DSTT into the NDS. Insert your microSD card into the DSTT. Turn on the NDS.[*]Run the DsttFlashChecker program to see if you have a real or a fake DSTT. If you have a fake DSTT and suspect that it may have been destroyed by the official fake-killer firmware, run the DsttFlashWriter program to re-flash your DSTT.[*]You should be able to run your games now. You can delete DsttFlashChecker.nds, DsttFlashWriter.nds, and DSTTDUMP.BIN from your microSD card if you want.[*]Always keep the following in mind:

Always leave some free space on your microSD card for save files and system files.

Always put games into your "games" folder. Also, put homebrew into a folder. Leave as few files as possible on the root of your microSD card.

Have you tried a different microSD reader or microSD card? The readers that come with these flash carts are notoriously crappy. Also, make sure you use "safely remove hardware" before removing your microSD card from your PC. And make sure you don't put too many files on the root of your microSD card -- put the games in a "games" folder. And make sure you leave plenty of free space on the microSD card for it to create system files and save files.